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- PDB-2vp5: Structural Studies of Nucleoside Analog and Feedback Inhibitor Bi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vp5 | ||||||
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Title | Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase | ||||||
![]() | DEOXYNUCLEOSIDE KINASE | ||||||
![]() | TRANSFERASE / ATP-BINDING / DNA SYNTHESIS / PHOSPHOPROTEIN / FEEDBACK INHIBITION / DEOXYRIBONUCLEOSIDE KINASE / SALVAGE PATHWAY / NUCLEOTIDE-BINDING / DTTP / KINASE / COMPLEX / DROSOPHILA | ||||||
Function / homology | ![]() deoxynucleoside kinase / Pyrimidine salvage / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity ...deoxynucleoside kinase / Pyrimidine salvage / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity / deoxynucleoside kinase activity / DNA biosynthetic process / kinase activity / phosphorylation / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mikkelsen, N.E. / Munch-Petersen, B. / Eklund, H. | ||||||
![]() | ![]() Title: Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase. Authors: Mikkelsen, N.E. / Munch-Petersen, B. / Eklund, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.8 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.1 KB | Display | ![]() |
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Full document | ![]() | 467.2 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jj8C ![]() 2vp0C ![]() 2vp2C ![]() 2vp4C ![]() 2vp6C ![]() 2vp9C ![]() 2vqsC ![]() 1j90S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper: (Code: given Matrix: (-0.9961, 0.002871, -0.08772), Vector: |
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Components
#1: Protein | Mass: 26906.707 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 48.53 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975501 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22045 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J90 Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.292 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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